Hello all,
I am setting up a 10 solvated systems. I am using a tleap to solvate the 10 peptides. As the proteins have different radii of gyration, each system has a different number of atoms.
I would like to use cpptraj to trim down the number of water residues while maintain a periodic box. I am calling cpptraj twice for the following reasons:
(1) Generate a .crd file with 315963 atoms
Input file called with 'cpptraj -p parm_wb_lambdaN_100.prmtop -i TrajIn1.in' :
trajin wb_lambdaN_100.crd
strip :WAT&!(:50000-155000)
trajout wb_strip_lambdaN_100.crd nobox
(2) Generate the corresponding .prmtop file
Input file called with 'cpptraj -p parm_wb_lambdaN_100.prmtop -i TrajIn2.in'
trajin wb_lambdaN_100.crd
parmstrip :WAT&!(:50000-155000)
parmwrite out wb_strip_lambdaN_100.prmtop
When I run these scripts and visualize in VMD, I am creating a solvated system that is not boxlike at all. Is there a easy way to do this?
I read about using the 'closest' command to keep a certain number of waters around a solute. However, I do not know of a way to generate a .prmtop file. It's been suggested on the forum (
http://archive.ambermd.org/201008/0537.html ) to create a pdb with ptraj, then move on to leap to generate a .prmtop via 'saveamberparm'. However, my system is over the number of atoms supported (99,999) within the .pdb format.
Thank you in advance for the help.
Joe Passman
University of Utah
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Received on Sun Feb 10 2013 - 17:30:02 PST
